Applying Mirror Modifier with Shape Keys on a rigged Model
For anyone who still wants to know (P.S. I did this in Blender 2.79):

This doesn't fix it entirely, but....

You can remove the mirror modifier,
and duplicate and then reverese the vertices onto the other side.

(E.g. move 3D cursor to centre of mesh, duplicate verts, and scale along x-axis by -1 around the 3D cursor)

Some of the shape keys might be close enough.
But some may need tweaking.

Depending on how lucky you are, this may or may not be easier than removing shape keys, applying mirror modifier, and re-do-ing all the shape keys again :/